Flaveria bidentis is an invasive plant found in large areas of northern China. This study conducted a separation and screening of the main functional bacteria in the soil of F. bidentis and investigated the change in the community structure. A variety of functional microbes were isolated using selective media and rep-PCR clustering, and a diversity analysis was carried out. In addition, the dominant populations of various functional bacteria were identified using 16S rRNA sequence alignment. The results showed that F. bidentis increased the contents of the major available nutrients in the soil, and the levels of azotobacteria, organic phosphorus bacteria, inorganic phosphorus bacteria, and silicate bacteria in the soil of F. bidentis were significantly higher than those of the native plant Tagetes erecta and the control. rep-PCR analysis indicated that the structure of the four functional bacterial microfloras in the soil of F. bidentis was significantly different from those of the native plant and control. The diversity analysis demonstrated that the diversity of functional microorganisms in the soil of F. bidentis was richer, the community structure was more complex, the predominant microflora comprised a greater proportion of the total population, and the ecological diversity was higher. This was further evidenced by identification of the main functional isolates from the three soil samples. Our findings indicated a mechanism of invasion by F. bidentis.